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Version skapad av Lars Arvestad 2015-11-06 08:48
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Working in Unix
The Unix compendium "An Introduction to Unix" is useful in this assignment.
In these assignments, you will need to use Unix redirection of input and output.
- Take a look at the large file /info/appbio15/data/gpcr.tab using head. This file contains data concerning G-coupled protein receptors from a number of species.head. How many columns are there (if you count by eye)?
If you work on your own computer: download this file to work on.
- How many lines is there in the file?
- Use grep and wc to find out how many human GPCRs there are listed. Do you search for "human" or "Homo sapiens"?
- How long is the shortest sequence listed in the same file? Use cut and sort!
- How many species are named in gpcr.tab?
- Use a for-loop to apply multi-sequence alignment program muscle to the data files in /info/appbio15/data/testatin/*.fa. If you work on your own computer: download this file (gzipped tar file) to work on.
- Figure out what muscle does and how you run it. (Sorry, no man-pages.)
- You have to use a for-loop in bash. Repeated manual invocation is not allowed in this course.
- Each run should have its own output file.
To present:
- You should be able to show and explain what you have done to the teacher.
- You are expected to understand how the commands work.